This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. A Startup allocation is requested for porting and testing the newly-developed Desmond molecular dynamics code to the Cray XT3 (Bigben) and Altix 4700 (Pople) at the Pittsburgh Supercomputing Center. Using this allocation, scientists at the PSC will work together with Desmond developers at D. E. Shaw Research to make the package freely available to users of PSC systems for non-commercial research activities. Desmond uses novel parallel algorithms and numerical techniques to enable the fast, scalable simulation of biomolecular systems and has enabled researchers to access the much longer timescales required to understand many important biological phenomena. On the Cray XT3 there is an opportunity to create a very efficient implementation of Desmond on the low-level Portals network interface. Due to the novel design of Desmond, it is anticipated that substantial effort will be required to port the code to run efficiently on these systems;however, successful completion of this project will provide the molecular dynamics research community with a powerful tool for the long time scale simulations of biomolecular systems.